BGE script error: Invalid Syntax
To write an if statement in python you need a colon at the end of the condition then the rest gets indented.
Like this

if a == b:
    print("yep")


So your code would be like this.

def toggleProne(): 
    if PlayerControls.playerMain['isInCover'] == 0:
        PlayerControls.playerMain['isCrouched'] = 0
        PlayerControls.playerMain['isStanding'] = 0
        PlayerControls.playerMain['isProne'] = 1
    return;


Personally, I would use a var for PlayerControls.playerMain, it would save you from having that whole thing four times.